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-   -   Ensembl vs NCBI (http://seqanswers.com/forums/showthread.php?t=9612)

GERALD 02-22-2011 08:43 AM

Ensembl vs NCBI
 
Could someone point me in the right direction to find documentation on ENSEMBL genomes vs NCBI genomes? Is ENSEMBL version 59 the same as hg19?

Jon_Keats 02-22-2011 09:12 AM

Quote:

Originally Posted by GERALD (Post 35595)
Could someone point me in the right direction to find documentation on ENSEMBL genomes vs NCBI genomes? Is ENSEMBL version 59 the same as hg19?

Sadly this information is not simple to find but I did go through the trouble of doing it once and have it on my introduction thread if you want to take my word for it. Sorry I can't exactly remember how I figured it out. (http://seqanswers.com/forums/showthr...?t=4589&page=2)

apfejes 02-22-2011 08:06 PM

For what it's worth, I've exported this from our local ensembl database. the last two digits tell you the reference version, the two digits before that are the ensembl version.

reference version 36, if I recall correctly, is hg18, reference 37 is hg19.

| homo_sapiens_core_38_36
| homo_sapiens_core_40_36b
| homo_sapiens_core_49_36k
| homo_sapiens_core_50_36l
| homo_sapiens_core_51_36m
| homo_sapiens_core_52_36n
| homo_sapiens_core_53_36o
| homo_sapiens_core_54_36p
| homo_sapiens_core_55_37
| homo_sapiens_core_56_37a
| homo_sapiens_core_57_37b
| homo_sapiens_core_58_37c
| homo_sapiens_core_59_37d
| homo_sapiens_core_60_37e
| homo_sapiens_core_61_37f

Giulietta 02-25-2011 04:37 AM

You can find the Ensembl assembly for different versions in the species (human) home page:

http://www.ensembl.org/Homo_sapiens/Info/Index

The current assembly in Ensembl is GRCh37, which is also hg19 (this is explained in the text on this page).

Click on 'View in archive site' at the bottom of this page for a list of Ensembl versions and the genome. In Ensembl 59, GRCh37 is used, which is also called hg19 by UCSC. GRCh37 is the official name from the Genome Reference Consortium:

http://www.ncbi.nlm.nih.gov/projects...an/index.shtml

UCSC used to name the human assembly hg18, but has included the official name in the newest assembly 'GRCh37/hg19'

http://genome.ucsc.edu/cgi-bin/hgTra...7695-133161157

NCBI also uses the official name "build 37.2", here:

http://www.ncbi.nlm.nih.gov/mapview/...y=homo+sapiens

The three projects strive to use the most updated reference assembly from the GRC. At the moment, they should all be in synch.

I hope this helps.


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